From: SourceForge.net <no...@so...> - 2011-12-21 21:41:22
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Bugs item #3463509, was opened at 2011-12-21 12:27 Message generated for change (Comment added) made by molusc2 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3463509&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Scripting Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Paul Pillot (molusc2) Assigned to: Bob Hanson (hansonr) Summary: show smiles not always providing Z/E isomer information Initial Comment: Using scribmol, I drew but-2-ene (cis-conformation) in chemdoodle. The corresponding 3D molecule is created by Jmol. "show smiles" gives : C/C=CC when transfered to cactus for optimization, the resulting 3D file is in trans configuration (the 2D mol file shows a crossed double bond) Sometimes (I can't find a reproductible scenario), when I draw the same molecule directly in Jmol, the "show smiles" gives : C(/C)=C/C which leads to a correct optimization. In trans configuration, the results are quite similar : "show smiles" gives C(/C)=CC which leads to a crossed double bond with cactus, but provides a molecule in trans configuration (I suppose it is the default) ---------------------------------------------------------------------- >Comment By: Paul Pillot (molusc2) Date: 2011-12-21 13:41 Message: I solved the aforementioned problem by using the jmolScriptWaitOutput method instead of JmolScriptWaitAsArray. The later strips backward slashes from the script messages. ---------------------------------------------------------------------- Comment By: Paul Pillot (molusc2) Date: 2011-12-21 12:59 Message: My bad ! The results aren't the same via the Jmol console and via the jmolScriptWait() method : backwards slashes are stripped which explains the loss of information. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3463509&group_id=23629 |